People also forget that while she is a Targaryen (which have been more allowing for female rulers), that she was the third child of Aerys II and Rhaella. In other words, she wasn't ever expected to rule and no one bothered to train her as such. Moreover, up-until the events of the first book, it was likely that she would have been Viserys' sister-wife in the Targaryen tradition. Also, the fact that she was essentially raised by Viserys as well since her mother died in childbirth, doesn't bode well for her education, especially given how horrid of a ruler Viserys would have been had he lived. Oh, and she was 14 in the beginning of the novels (I think 16/17 for the TV series). Basically, she was never considered to be a ruler and wasn't trained to be one. Essentially, she had nothing to go on to knowing how to rule, except for the advice of an exiled knight. All she learned as a leader was through trial and error. Let's also factor in the fact that people were half-expecting her to be insane like daddy-dearest as well.
All these facts taken together shows that as a leader, the stacks were not in her favour. Yet, she grows and learns from her mistakes. Hell, if you want to compare her to someone look at Joffrey. He was raised (albeit Cersei played her hand in there as well) since childhood to be king and he's wretched one at that. I'd take Dany over Joffrey anyday. At least Dany tries and resembles a human being in the process.